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BioC 3.1: CHECK report for conumee on morelia

This page was generated on 2015-10-09 09:42:55 -0700 (Fri, 09 Oct 2015).

Package 209/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conumee 1.0.0
Volker Hovestadt
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/conumee
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: conumee
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings conumee_1.0.0.tar.gz
StartedAt: 2015-10-09 00:41:31 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:00:58 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 1166.7 seconds
RetCode: 0
Status:  OK 
CheckDir: conumee.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings conumee_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/conumee.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘conumee/DESCRIPTION’ ... OK
* this is package ‘conumee’ version ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘conumee’ can be installed ... [21s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CNV.load,matrix : .local: no visible binding for global variable ‘anno’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15m/16m] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
CNV.detailplot      109.586  8.418 121.270
CNV.detailplot_wrap 109.205  7.447 120.482
CNV.analysis-class   99.229  7.073 108.716
CNV.genomeplot       86.686  6.941  94.998
CNV.write            79.901  6.402  91.362
CNV.segment          66.590  3.711  71.266
CNV.bin              56.261  5.767  62.411
CNV.detail           55.009  5.678  61.058
CNV.anno-class       52.476  5.135  58.248
CNV.create_anno      50.104  4.767  55.278
CNV.fit              46.510  4.404  50.921
read.450k.url         4.340  0.564  39.167
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/conumee.Rcheck/00check.log’
for details.


conumee.Rcheck/00install.out:

* installing *source* package ‘conumee’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (conumee)

conumee.Rcheck/conumee-Ex.timings:

nameusersystemelapsed
CNV.analysis-class 99.229 7.073108.716
CNV.anno-class52.476 5.13558.248
CNV.bin56.261 5.76762.411
CNV.create_anno50.104 4.76755.278
CNV.data-class1.3550.2871.647
CNV.detail55.009 5.67861.058
CNV.detailplot109.586 8.418121.270
CNV.detailplot_wrap109.205 7.447120.482
CNV.fit46.510 4.40450.921
CNV.genomeplot86.686 6.94194.998
CNV.load1.4100.2962.178
CNV.segment66.590 3.71171.266
CNV.write79.901 6.40291.362
read.450k.url 4.340 0.56439.167